A 72-Hour Tokyo Eating Tour

Sea urchin, soba and a melt-in-your-mouth omelet—on a stopwatch

A year after moving from Tokyo to San Francisco, my husband and I craved good Japanese food so much that we ditched our families for Thanksgiving and flew to Japan for three nights of eating.

San Francisco isn't exactly a culinary wasteland. It has great wine, an abundance of fresh produce and many good restaurants. But in Tokyo, restaurants create beautiful dishes that are assembled to play up the natural flavor of seasonal ingredients like bamboo shoots in the spring and pike eel in the summer. After months of fruitlessly seeking a San Francisco restaurant that would give us a taste of that experience, we decided we had no choice but to travel.

Tasting Tokyo

See photos from the trip.

A sobu meal at Hakone Akatsukian. Geoff Johnson for The Wall Street Journal

Autumn—known as the season for strong appetites in Japan—was the ideal time to take the trip because of the abundance of seasonal foods like mushrooms, scallops, persimmons and delicious bonito fish, fattened up after a summer of feeding.

So my husband Patrick and I put together a 72-hour itinerary of multiple dinners, and a trip to a hot-springs inn an hour away from Tokyo. Our goal was to pack in as many of our favorite restaurants (strictly Japanese ones) as possible. Multiple sushi meals and tempura were musts. And while it's possible to eat well on a budget in Tokyo, the brevity of our trip led us to throw cost to the wind. Lunches cost roughly $10 to $20, but we calculated dinners would cost $200 (about 18,200 yen) or more per person including drinks.

Day 1: Sea Urchin and Bordeaux

Patrick and I left San Francisco on Thanksgiving morning, which got us into Tokyo on Friday afternoon, in time for dinner. The journey—15 hours door-to-door—was all worth it as soon as we took a bite of the deep-fried tofu skin layered with mountain potato chips at Taku, a tiny sushi restaurant discreetly located in our old neighborhood in central west Tokyo. That was the start to an almost 30-course meal of bite-sized dishes including uni, or sea urchin, from Japan's northernmost island of Hokkaido, and a white fish called halfbeak that was gently steam-grilled between bamboo leaves.

So Many Menus, So Little Time

UOGASHI SENRYOU

This hole in the wall in a maze of restaurants will (if you can find it) have menus in English. The specialty is the Kaisen Hitsumabushi: a mixture of rice and more than 12 kinds of fish and shellfish for 2,100 yen (about $23).

SUSHI TEMPURA AKI

The restaurant is elegantly divided into sections for sushi and tempura. The sushi is good, but we come here for the tempura, made by the former head chef of the famous tempura restaurant at the Yamanoue (also known as Hilltop) Hotel. Meals can cost from 15,000 yen to 20,000 yen a person.

Elevage

4-2-13 Nishi-Azabu, 2Fl; +81-3-6419-3889

A big choice of rare wines by the glass as well as spirits. The tiny bar (two tables and a counter) is a bit tight but coveted by connoisseurs.

HORAI

Until recently a member of the Relais and Château network, this hot-springs inn boasts traditional-style architecture, two beautiful outdoor baths overlooking the Pacific and its classically Japanese kaiseki (formal course) cuisine. Rates start at about 34,000 yen per person including dinner and breakfast (drinks are separate).

NISHI-AZABU TAKU

SHOMIN

4-22-8 Nishi-Azabu; +81-3-3400-1666

The specialty is oden, a winter dish of daikon radish and various processed fishcakes, fishballs and meatballs in a light dashi broth. Also the yakitori (grilled chicken on skewers) and grilled riceballs. Open until early morning, the place gets crowded after 10 p.m.

KYUBEY

Kyubey is one of the top sushi restaurants in Tokyo. The restaurant only takes reservations for the 11:30 seating for lunch (prices start 8,400 yen) or seatings between 5 p.m. and 7 p.m. for dinner (starting at 15,750 yen). To avoid a surprise bill at the end, order sets off the printed menu.

After a brief stop at wine bar Elevage where I had a 1982 Bordeaux, we concluded the evening at Shomin, a traditional Japanese izakaya bar that serves little plates of food with drinks. We stayed up long enough to have another drink and a snack of grilled rice ball, crunchy and toasted on the outside and moist on the inside and flavored with soy sauce. By the time we got back to our hotel it was 1:30 a.m.

Day 2: The Joy of Soba

A mere seven hours later, we were at the Tsukiji Fish Market, the world's largest. Our favorite sushi bar inside the market was packed, so we ended up at Uogashi Senryou in the outer market. Their specialty: a three-in-one rice dish topped with many kinds of raw seafood, including uni, salmon roe and small pieces of tuna. The first serving is eaten by itself with soy sauce and wasabi, the second serving is mixed together with chopped braised vegetables, and the third is eaten in a light broth. The dish, known as hitsumabushi, is a take on the traditional version made with cooked eel.

After that heavy breakfast, our plan was to have a light soba lunch at another old standby, Hakone Akatsukian, near Roppongi, which is famous for its nightlife. But temptation got the better of us, and we ordered soba sets with a square of fresh tofu and a side of tempura vegetables. True aficionados swear by zaru soba, or cold noodles dipped in a broth, rather than the hot noodle soup better known in the U.S., to fully appreciate the chewiness and the earthy buckwheat flavor. The dark dipping broth is later diluted with the hot water that the soba was cooked in to make a simple soup.

The second day concluded with a lavish tempura dinner at Sushi Tempura Aki in eastern Tokyo, where our favorite chef served us lightly battered vegetables and seafood gently fried in 100% pure sesame oil and placed before us one by one. Real tempura is nothing like the greasy, batter-heavy version that is common outside Japan. Highlights included a fresh scallop that was fried so quickly that it was still raw on the inside to preserve its delicate flavor.

The challenge of planning a weekend trip to Japan is what to eat on Sundays, when most restaurants that are serious about food are closed because the fish market is shut. Our solution was to hop on the bullet train and travel to the seaside city of Atami, about an hour from Tokyo. We planned to spend a night at Horai, an old hot-springs inn known for lavish meals.

After soaking in big baths overlooking the Pacific Ocean, we were treated to a 10-course meal in our room that started with a sesame tofu and clear soup. That was followed by an array of sashimi including langoustine slices that were so recently cut that the head we were presented with was still twitching. After more courses that included a deep-fried rice cake with radish sauce and grilled scallops, we finished simply with a steamed bowl of rice, miso soup and pickled vegetables.

Day 3: Ginza Gourmands

The next morning, the inn made a miso soup for us with the head of the langoustine. That accompanied a traditional breakfast of grilled fish, vegetables, rice and a small omelet made with a delicate broth.

After breakfast, we sped back to Tokyo for lunch—our final meal of the trip. Kyubey in the tony Ginza district is one of the city's most venerable sushi establishments, favored by countless politicians, executives and Hollywood stars like Will Smith. Rare for a restaurant of its caliber, Kyubey has several locations mostly in Tokyo, which gives them the scale to afford the highest-quality fish (the owner made news earlier this month when he participated in the purchase of a bluefin tuna for $175,000). When we sat down, head chef Mr. Taira immediately served us bright orange pearls of marinated salmon roe in a small bowl as we informed him that we were there for the dinner course.

Taking up the challenge, he served translucent slices of various white fish, bonito stuffed with minced garlic and scallions, and a mixture of minced Japanese mackerel, miso, chopped scallions and ginger known as "Namero", which is loosely translated as "plate-licking good."

After cleansing our palates with a sandwich of thinly sliced radish and sour plum paste, we moved onto sushi. The sea urchin was sweet and creamy, the seared tuna fatty and flavorful and the raw shrimp so fresh that they were jumping off the counter as they waited to be peeled.

As we wondered how we could get on an eight-hour plane ride after the meal, Mr. Taira pushed one final square of melt-in-your-mouth omelet on us. "Think of it as dessert," he said.

Corrections & Amplifications Oden, a specialty at the Tokyo restaurant Shomin, contains fishballs. A previous version of this story erroneously said the dish contains flashballs.

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